tbuckley/cabot-search huggingface dataset:
Abstract 2882: Characteristic immunomodulatory role of myeloid galectin-9 in the brain tumor microenvironment
Authors: Chanju Lee, Dahee Yu, Eun Jung Park
Journal: Cancer Research (2023)

Abstract Galectin-9 is a member of galectin family with carbohydrate-recognition domains that specifically bind to β-galactoside. Increasing reports have suggested that galectin-9 can bind and interact with immune-modulatory molecules including TIM-3 in several pathophysiological conditions, especially in T cells. However, to date, little is known about the galectin-9 in myeloid cells under tumor microenvironment. In this study, we explored the expressional characteristics and roles of galectin-9 in the brain tumor microenvironment using an intracranial mouse brain tumor model and in vitro system. We found that expression level of galectin-9 was markedly elevated in ipsilateral hemisphere compared to contralateral hemisphere of intracranial brain tumor model. FACS analyses showed that galectin-9 expression was higher in CD45highCD11bhigh macrophages and CD45midCD11bhigh microglia as well as lymphocytes from ipsilateral region than those from contralateral region. In addition, galectin-9 levels were increased after exposure to GL26 brain tumor cells in in vitro co-culture system using primary microglia. Interestingly, phagocytic activity, a key function of myeloid cells, was significantly reduced in galecin-9+ microglia compared to galecin-9- microglia when co-cultured with GL26-GFP cells. Furthermore, SIRPα levels were higher in galectin-9+ microglia than galecin-9- microglia. Similar results were observed in macrophages. Collectively, these findings suggest that galectin-9 may be an important modulatory molecule in myeloid cells under brain tumor microenvironment. Citation Format: Chanju Lee, Dahee Yu, Eun Jung Park. Characteristic immunomodulatory role of myeloid galectin-9 in the brain tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2882.
Abstract 4718: Analyses of epigenetic marks and mechanisms in disease: Your guide to a successful CUT&amp;RUN assay
Authors: Angela H. Guo, Christopher R. Comeau, Fang Chen, Christopher J. Fry
Journal: Cancer Research (2023)

Abstract Like the chromatin immunoprecipitation (ChIP) assay, Cleavage Under Targets &amp; Release Using Nuclease (CUT&amp;RUN) is a powerful and versatile technique used for probing protein-DNA interactions within the natural chromatin context of the cell. The CUT&amp;RUN assay can be combined with downstream qPCR or NG-seq to analyze histone modifications and binding of transcription factors, DNA replication factors, or DNA repair proteins at specific target genes or across the entire genome. CUT&amp;RUN provides a rapid, robust, and true low cell number assay for detection of protein-DNA interactions in the cell. Unlike the ChIP assay, CUT&amp;RUN is free from formaldehyde cross-linking, chromatin fragmentation, and immunoprecipitation. Previously, we have shown that, compared to ChIP, CUT&amp;RUN requires fewer starting cells (100K), has a much faster protocol (one day from cells to DNA), generates lower background signal (requires less sequencing depth), and offers spike-in control DNA for effective normalization of signal between samples and between experiments. We recently updated the CST CUT&amp;RUN Assay Kit for use with 5,000-20,000 cells and added protocols for fixed cells and tissue. I will discuss the basics of the CUT&amp;RUN assay and important factors to consider when setting up your experiment. In addition, I will provide data showing the versatility of this assay for mapping various histone modifications, transcription factor, and transcription cofactor binding across multiple sample types. Finally, I will discuss how the general protocol is optimized for greater signal to noise ratio, reduced number of starting cells, and provide an alternative digestion method to prepare the input DNA as a critical control of the CUT&amp;RUN experiment. Citation Format: Angela H. Guo, Christopher R. Comeau, Fang Chen, Christopher J. Fry. Analyses of epigenetic marks and mechanisms in disease: Your guide to a successful CUT&amp;RUN assay. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4718.
Abstract 2447: XPC suppresses cancer stem cells via inhibiting STAT1-mediated expression of SOX2 in NSCLC
Authors: Na Li, Xuetao Bai, Shurui Cai, Ananya Banerjee, Yajing Yang, Qianyun Ge, Linzhou Wang, Qi-En Wang
Journal: Cancer Research (2023)

Abstract Xeroderma pigmentosum group C (XPC) is a DNA repair factor mainly involved in nucleotide excision repair but also has functions beyond its role in DNA repair. More than 60% lung adenocarcinoma patients exhibit XPC copy number deletions, and among these patients, low XPC expression is correlated with a poor outcome, indicating that XPC may play a critical role in preventing lung cancer progression. Here, we revealed an inverse relationship between XPC expression and the abundance of cancer stem cell (CSC) subpopulation in non-small cell lung cancer (NSCLC). We demonstrated that knockdown of XPC leads to larger CSC subpopulations in lung cancer cells, while overexpression of XPC can inhibit the stemness properties of these cells. The RNA-seq analysis suggested that XPC can suppress the expression of SOX2, a critical stem cell-specific transcription factor. This finding was further validated in multiple NSCLC cell lines at both mRNA and protein levels. To further investigate the mechanism underlying XPC-mediated suppression of SOX2 expression, we performed quantitative proteomics combined with immuno-affinity purification and found that XPC can interact with STAT1, which is a transcription factor of SOX2. Moreover, XPC can inversely regulate the activation of STAT1 (pSTAT1-Y701), indicating that XPC may suppress SOX2 expression via inhibiting the STAT1 signaling. Taken together, we identified a novel mechanism behind poor outcomes of NSCLC patients with haploinsufficiency XPC. Low level of XPC in lung cancer cells de-represses the activity of STAT1, which further promotes the expression of stem cell-specific gene SOX2 and facilitates the maintenance of CSC subpopulations. Given that CSCs are believed to contribute to tumor progression and chemoresistance, enhanced stemness and expanded CSC populations in XPC haploinsufficiency NSCLC could be responsible for the poor outcome of these patients. Citation Format: Na Li, Xuetao Bai, Shurui Cai, Ananya Banerjee, Yajing Yang, Qianyun Ge, Linzhou Wang, Qi-En Wang. XPC suppresses cancer stem cells via inhibiting STAT1-mediated expression of SOX2 in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2447.
Abstract 3865: Multiple cancer types rapidly escape from multiple MAPK inhibitors to generate mutagenesis-prone subpopulations
Authors: Timothy E. Hoffman, Chen Yang, Varuna Nangia, Christopher Ryland Ill, Sabrina L. Spencer
Journal: Cancer Research (2023)

Abstract Many cancers harbor pro-proliferative mutations of the mitogen-activated protein kinase (MAPK) pathway and many targeted inhibitors now exist for clinical use, but drug resistance remains a major issue. We previously showed that BRAF-driven melanoma cells treated with BRAF inhibitors can non-genetically adapt to drug within 3-4 days to escape quiescence and resume slow proliferation. Here we show that this phenomenon is not unique to melanomas treated with BRAF inhibitors but rather is widespread across many clinical MAPK inhibitors and cancer types driven by EGFR, KRAS, and BRAF mutations. In all treatment contexts examined, a subset of cells can escape drug-induced quiescence within four days to resume proliferation. These escapee cells broadly experience aberrant DNA replication, accumulate DNA lesions, spend longer in G2-M cell cycle phases, and mount an ATR-dependent stress response. We further identify the Fanconi anemia (FA) DNA repair pathway as critical for successful mitotic completion in escapees. Long-term cultures, patient samples, and clinical data demonstrate a broad dependency on ATR- and FA-mediated stress tolerance. Together, these results highlight the pervasiveness with which MAPK-mutant cancers are able to rapidly escape drug and the importance of suppressing early stress tolerance pathways to potentially achieve more durable clinical responses to targeted MAPK pathway inhibitors. Citation Format: Timothy E. Hoffman, Chen Yang, Varuna Nangia, Christopher Ryland Ill, Sabrina L. Spencer. Multiple cancer types rapidly escape from multiple MAPK inhibitors to generate mutagenesis-prone subpopulations. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3865.
Abstract 3401: Discovery of GH658, a novel tead allosteric inhibitor as a cancer therapy
Authors: Jie Jack Li, Guiping Zhang, Jiapeng Li
Journal: Cancer Research (2023)

Abstract The Hippo pathway is an evolutionarily conserved signaling cascade. Its dysregulation may lead to cancer progression, metastasis, cancer therapy resistance, and immune evasion. Diverse genetic aberrations leading to YAP/TAZ hyperactivation have been elucidated over the last 20 years. Almost all the pro-tumor mutations lead to constitutive TEAD transcription factor activation, suggesting that targeting TEAD transcription factors could offer an important therapeutic opportunity. Employing structure-based drug design, we have discovered GH658, a novel allosteric TEAD inhibitor that selectively targets the auto-palmitoylation pocket of TEAD proteins. In vitro, GH658 displayed a low nM potency in TEAD-based reporter assays, which translated to specific low nM inhibition of NF2 deficient mesothelioma proliferation. In vivo, GH658 demonstrated favorable pharmacokinetic properties in different species and showed acceptable safety profile. Furthermore, daily oral dosing of GH658 led to complete growth inhibition of NF2 mutant xenograft tumors without adverse effect on body weight. More importantly, GH658 displayed significant in vivo effect on drug tolerant persistent cancer cells and drug resistance against inhibitors targeting EGFR‒RAS signaling pathways in combination studies. In summary, with potent in vitro and in vivo efficacy of targeting YAP/TAZ‒TEAD transcriptional complex, GH658 not only showed consistent monotherapy activity in selected cancer models, but also demonstrated significant synergistic effects in diverse drug combination studies. Citation Format: Jie Jack Li, Guiping Zhang, Jiapeng Li. Discovery of GH658, a novel tead allosteric inhibitor as a cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3401.
Abstract 3020: Machine learning-based cluster analysis of immune cell subtypes and breast cancer survival
Authors: Zhanwei Wang, Dionyssios Katsaros, Junlong Wang, Nicholetta Biglio, Brenda Y. Hernandez, Peiwen Fei, Lingeng Lu, Harvey Risch, Herbert Yu
Journal: Cancer Research (2023)

Abstract Background: Host immunity involves various immune cells working in concert to achieve balanced immune response. Host immunity interacts with tumorigenic process impacting disease outcome. Clusters of different immune cells may indicate specific host-tumor interplay. Identifying the clusters may reveal unique host immunity in response to tumor growth. Methods: CIBERSORT was used to estimate relative abundances of 22 immune cell types in 3 datasets, METABRIC, TCGA, and our study. The cell type data in METABRIC were analyzed for cluster using unsupervised hierarchical clustering (UHC). The UHC results were employed to train machine learning models, random forest (RF), deep neural network (DNN), stepAIC, and elastic net. Kaplan-Meier and Cox regression survival analyses were performed to assess cell clusters in association with relapse-free and overall survival. Differentially expressed genes (DEGs) by immune cell clusters were interrogated with IPA for molecular signatures. Results: UHC analysis identified two distinct immune cell clusters, clusters A (83.2%) and B (16.8%). Memory B cells, plasma cells, CD8 positive T cells, resting memory CD4 T cells, activated NK cells, monocytes, M1 macrophages, and resting mast cells were more abundant in clusters A than B, whereas regulatory T cells and M0 and M2 macrophages were more in clusters B than A. Patients in cluster A had favorable survival compared to those in cluster B. Similar survival associations were also observed in TCGA and our study when using a RF model trained with the UHC results. The survival associations were independent from clinicopathological variables. IPA analysis showed that pathogen-induced cytokine storm signaling pathway, phagosome formation, and T cell receptor signaling were related to the cell type clusters. Conclusions: Our finding suggests that different immune cell clusters may indicate distinct immune responses to tumor growth, suggesting their potential for disease management. Citation Format: Zhanwei Wang, Dionyssios Katsaros, Junlong Wang, Nicholetta Biglio, Brenda Y. Hernandez, Peiwen Fei, Lingeng Lu, Harvey Risch, Herbert Yu. Machine learning-based cluster analysis of immune cell subtypes and breast cancer survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3020.
Abstract 4964: SW-682: A novel TEAD inhibitor for the treatment of cancers bearing mutations in the Hippo signaling pathway
Authors: Lei Chen, Paula Milani de Marval, Kendall Powell, Mark Johnson, Greg Falls, Brian Lawhorn, Aurélie Candi, Amuri Kilonda, Bart Vanderhoydonck, Arnaud Marchand, Matthias Versele, Georg Halder, Stephen L. Gwaltney, Adeela Kamal
Journal: Cancer Research (2023)

Abstract Many cancers harbor mutations in the Hippo pathway that lead to constitutive activation of the transcriptional co-activators YAP/TAZ that then bind the transcription factor TEAD and drive aberrant transcription of target genes involved in cell proliferation and tumor progression. Hyperactivation of YAP/TAZ has also been associated with resistance to targeted therapies, including MAPK pathway inhibitors. To target cancers that bear mutations in the Hippo pathway or are resistant to therapies due to YAP/TAZ activation, we developed SW-682, a pan-TEAD small molecule inhibitor that blocks TEAD-dependent transcription by binding to the palmitoylation pocket of all TEAD isoforms. In vitro, SW-682 inhibited the proliferation of human Hippo-mutant mesothelioma cells with nanomolar potency, with little to no effect on Hippo wild-type tumor cells. SW-682 down-regulated TEAD-dependent reporter gene expression in a dose-dependent manner, while having no effect on reporters monitoring other pathways. In vivo, daily oral administration of SW-682 to adult mice resulted in tumor regression in Hippo-mutant mesothelioma models and caused down-regulation of expression of the TEAD-dependent genes CCN1 and CCN2 and a YAP gene signature, as measured by qPCR or RNA-seq analysis. SW-682 has a favorable PK profile with good oral bioavailability in the mouse and was well tolerated with no signs of body weight loss. To test the hypothesis that TEAD inhibition can overcome YAP-driven resistance mechanisms, we explored SW-682 in combination with MEK inhibitors in several in vitro and ex vivo patient-derived tumor models including BRAF and NRAS mutated melanoma. Moreover, to identify new indications that may benefit from TEAD inhibition, we screened patient-derived 3D organoid tumor cells and matching patient-derived xenograft models that have been molecularly profiled. In summary, SW-682 is a potent and selective investigational TEAD inhibitor which demonstrated anti-tumor effects in models harboring aberrant expression of the Hippo pathway, suggesting therapeutic potential in multiple Hippo-mutant solid tumors. Citation Format: Lei Chen, Paula Milani de Marval, Kendall Powell, Mark Johnson, Greg Falls, Brian Lawhorn, Aurélie Candi, Amuri Kilonda, Bart Vanderhoydonck, Arnaud Marchand, Matthias Versele, Georg Halder, Stephen L. Gwaltney, Adeela Kamal. SW-682: A novel TEAD inhibitor for the treatment of cancers bearing mutations in the Hippo signaling pathway. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4964.
Abstract 1354: Proteasome activation prevents T cell exhaustion and improves antitumor activity
Authors: Ander de Blas, Massimo Andreatta, Asier Antoñana-Vildosola, Paloma Velasco, Leire Egia-Mendikute, Borja Jimenez-Lasheras, Samanta Romina Zanetti, Santiago J. Carmona, Endika Prieto-Fernández, Asis Palazon
Journal: Cancer Research (2023)

Abstract Tumor infiltrating lymphocytes (TILs) exert their antitumor activity in the tumor microenvironment (TME). Chronic TCR stimulation, together with features of the tumor microenvironment such as hypoxia, result in T cell exhaustion. Exhausted T cells (TEX) are characterized by oxidative stress that leads to cellular accumulation of oxidized proteins. Because the proteasome complex clears oxidized proteins, we hypothesized that its capacity might be overloaded in TEX, limiting their fitness. Analysis of single-cell transcriptomics data from 19 tumor types indicated an increased proteasome activity in TEX compared to non-exhausted TILs. Higher levels of ROS-induced protein oxidation, expression of proteasome genes and proteasome activity were confirmed in human TEX, suggesting that increased proteasome activity might be a compensatory mechanism to exhaustion-associated oxidative stress. We show that pharmacological activation of the proteasome prevented T cell exhaustion, and lead to superior anti-tumor control in the context of adoptive cell therapy in mouse models. Thus, modulation of the proteasome activity is an attractive strategy to prevent T cell dysfunction promoted by the TME, and to potentially overcome this major obstacle in cancer immunotherapies against solid tumors. Citation Format: Ander de Blas, Massimo Andreatta, Asier Antoñana-Vildosola, Paloma Velasco, Leire Egia-Mendikute, Borja Jimenez-Lasheras, Samanta Romina Zanetti, Santiago J. Carmona, Endika Prieto-Fernández, Asis Palazon. Proteasome activation prevents T cell exhaustion and improves antitumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1354.
Abstract 2455: Investigating cancer stem cell plasticity in ovarian cancer
Authors: Tara X. Metcalfe, Shu Zhang, Christiane Hassel, Heather M. O'Hagan, Kenneth P. Nephew
Journal: Cancer Research (2023)

Abstract Most women diagnosed with late-stage high grade serous ovarian cancer (HGSOC) develop recurrent, platinum-resistant tumors. Ovarian cancer stem cells (OCSCs) are hypothesized to contribute to the emergence of these resistant tumors. CSCs have been postulated to reside in a plastic state, which can allow for the conversion of non-CSC to CSC. This process of dedifferentiation continues during tumor development and chemotherapeutic agents like platinum can exaggerate CSC plasticity. We have previously demonstrated that acute platinum treatment enriched for OCSCs. However, whether platinum transforms non-OCSCs into OCSCs to contribute to this subpopulation of cells remains unclear, and the underlying mechanism remains incompletely understood. To examine OCSC plasticity, aldehyde dehydrogenase (ALDH; functional marker) and fluorescence activated cell sorting were used to isolate OCSCs (ALDH+) and non-OCSCs (ALDH-) from HGSOC cell lines, OVCAR5 and OVCAR3. To determine the stability of the non-OCSC phenotype, ALDH- cells were cultured for 3 and 5 days and ALDH activity was measured using flow cytometry. At both timepoints examined, ALDH- cells remained ALDH-, with approximately less than 1% being ALDH+ (p&amp;lt;0.05). To determine if platinum can induce conversion of non-OCSC to OCSC, ALDH- cells were treated with cisplatin (12µM for 16h), and the percent of ALDH+ cells was measured using flow cytometry. Treatment of ALDH- cells with cisplatin resulted in conversion of approximately 3-4% of ALDH- cells into ALDH+ cells (p&amp;lt;0.05). Furthermore, increased expression (p&amp;lt;0.05) of stemness genes BMI1, NANOG, OCT4, and SOX2, analyzed using qRT-PCR, was observed in converted OCSCs compared to parental ALDH+ and whole cell populations treated with cisplatin (12µM for 16h), suggesting that platinum induced the observed differences in the stemness phenotype. With the goal of targeting key genes and pathways to inhibit platinum-induced OCSC conversion, we are carrying out RNA-sequencing analysis of the converted OCSCs and investigating the genes and pathways driving the platinum-induced conversion on non-OCSCs to OCSCs. Understanding the mechanisms involved in OCSC plasticity is critical to developing targeted therapies to block the persistence of OCSCs and ultimately reduce mortality in patients. Citation Format: Tara X. Metcalfe, Shu Zhang, Christiane Hassel, Heather M. O'Hagan, Kenneth P. Nephew. Investigating cancer stem cell plasticity in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2455.